[2023-06-30 20:55:21,829] [INFO] DFAST_QC pipeline started.
[2023-06-30 20:55:21,837] [INFO] DFAST_QC version: 0.5.7
[2023-06-30 20:55:21,838] [INFO] DQC Reference Directory: /var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference
[2023-06-30 20:55:24,603] [INFO] ===== Start taxonomy check using ANI =====
[2023-06-30 20:55:24,605] [INFO] Task started: Prodigal
[2023-06-30 20:55:24,605] [INFO] Running command: gunzip -c /var/lib/cwl/stg2e70a685-ec51-4148-899b-6ceccc69e6bd/GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna.gz | prodigal -d GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/cds.fna -a GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/protein.faa -g 11 -q > /dev/null
[2023-06-30 20:55:27,128] [INFO] Task succeeded: Prodigal
[2023-06-30 20:55:27,129] [INFO] Task started: HMMsearch
[2023-06-30 20:55:27,129] [INFO] Running command: hmmsearch --tblout GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/hmmer_result.tsv -E 1E-50 /var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference/reference_markers.hmm GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/protein.faa > /dev/null
[2023-06-30 20:55:27,339] [INFO] Task succeeded: HMMsearch
[2023-06-30 20:55:27,340] [WARNING] Found 3/6 markers. [/var/lib/cwl/stg2e70a685-ec51-4148-899b-6ceccc69e6bd/GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna.gz]
[2023-06-30 20:55:27,363] [INFO] Query marker FASTA was written to GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/markers.fasta
[2023-06-30 20:55:27,364] [INFO] Task started: Blastn
[2023-06-30 20:55:27,364] [INFO] Running command: blastn -query GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/markers.fasta -db /var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference/reference_markers.fasta -out GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/blast.markers.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:28,524] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:28,529] [INFO] Selected 11 target genomes.
[2023-06-30 20:55:28,530] [INFO] Target genome list was writen to GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/target_genomes.txt
[2023-06-30 20:55:28,537] [INFO] Task started: fastANI
[2023-06-30 20:55:28,537] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e70a685-ec51-4148-899b-6ceccc69e6bd/GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna.gz --refList GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/target_genomes.txt --output GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/fastani_result.tsv --threads 1
[2023-06-30 20:55:34,826] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:34,827] [INFO] Loading species specific ANI threshold from /var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt
[2023-06-30 20:55:34,828] [WARNING] Species-specific ANI threshold file not found. Will use the default threshold for all species. [/var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference/prokaryote_ANI_species_specific_threshold.txt]
[2023-06-30 20:55:34,830] [INFO] Found 0 fastANI hits (0 hits with ANI > threshold)
[2023-06-30 20:55:34,830] [INFO] The taxonomy check result is classified as 'no_hit'.
[2023-06-30 20:55:34,831] [INFO] DFAST Taxonomy check final result
--------------------------------------------------------------------------------
organism_name	strain	accession	taxid	species_taxid	relation_to_type	validated	ani	matched_fragments	total_fragments	ani_threshold	status
--------------------------------------------------------------------------------
[2023-06-30 20:55:34,833] [INFO] DFAST Taxonomy check result was written to GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/tc_result.tsv
[2023-06-30 20:55:34,834] [INFO] ===== Taxonomy check completed =====
[2023-06-30 20:55:34,835] [INFO] ===== Start completeness check using CheckM =====
[2023-06-30 20:55:34,835] [INFO] Setting CHECKM_DATA_PATH to /var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference/checkm_data
[2023-06-30 20:55:34,841] [INFO] Selected 'Prokaryote' markers (life, taxid=0) for CheckM
[2023-06-30 20:55:34,859] [INFO] Task started: CheckM
[2023-06-30 20:55:34,859] [INFO] Running command: checkm taxonomy_wf --tab_table -f GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/cc_result.tsv -t 1 life "Prokaryote" GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/checkm_input GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/checkm_result
[2023-06-30 20:55:50,876] [INFO] Task succeeded: CheckM
[2023-06-30 20:55:50,877] [INFO] Completeness check finished.
--------------------------------------------------------------------------------
Completeness: 51.04%
Contamintation: 0.00%
Strain heterogeneity: 0.00%
--------------------------------------------------------------------------------
[2023-06-30 20:55:50,896] [INFO] ===== Completeness check finished =====
[2023-06-30 20:55:50,897] [INFO] ===== Start GTDB Search =====
[2023-06-30 20:55:50,897] [INFO] Query marker FASTA already exists. Will reuse it. (GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/markers.fasta)
[2023-06-30 20:55:50,898] [INFO] Task started: Blastn
[2023-06-30 20:55:50,898] [INFO] Running command: blastn -query GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/markers.fasta -db /var/lib/cwl/stg4941c855-0b70-4b98-aa4f-599fea204e0e/dqc_reference/reference_markers_gtdb.fasta -out GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/blast.markers.gtdb.tsv -outfmt 6 -max_hsps 1 -num_alignments 5
[2023-06-30 20:55:51,685] [INFO] Task succeeded: Blastn
[2023-06-30 20:55:51,690] [INFO] Selected 6 target genomes.
[2023-06-30 20:55:51,691] [INFO] Target genome list was writen to GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/target_genomes_gtdb.txt
[2023-06-30 20:55:51,696] [INFO] Task started: fastANI
[2023-06-30 20:55:51,696] [INFO] Running command: fastANI --query /var/lib/cwl/stg2e70a685-ec51-4148-899b-6ceccc69e6bd/GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna.gz --refList GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/target_genomes_gtdb.txt --output GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/fastani_result_gtdb.tsv --threads 1
[2023-06-30 20:55:53,133] [INFO] Task succeeded: fastANI
[2023-06-30 20:55:53,144] [INFO] Found 6 fastANI hits (1 hits with ANI > circumscription radius)
[2023-06-30 20:55:53,144] [INFO] GTDB search result
--------------------------------------------------------------------------------
accession	gtdb_species	ani	matched_fragments	total_fragments	gtdb_taxonomy	ani_circumscription_radius	mean_intra_species_ani	min_intra_species_ani	mean_intra_species_af	min_intra_species_af	num_clustered_genomes	status
GCA_903867285.1	s__PALSA-747 sp903867285	99.4478	210	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	98.56	98.05	0.76	0.69	12	conclusive
GCA_903827345.1	s__PALSA-747 sp903827345	87.8308	168	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	97.69	97.69	0.77	0.77	2	-
GCA_903933585.1	s__PALSA-747 sp903933585	85.3468	206	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.42	99.37	0.91	0.88	4	-
GCA_903899375.1	s__PALSA-747 sp903899375	83.0561	176	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	99.46	99.00	0.86	0.79	59	-
GCA_903932705.1	s__PALSA-747 sp903932705	78.0673	62	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
GCA_903839355.1	s__PALSA-747 sp903839355	77.6734	55	250	d__Bacteria;p__Actinobacteriota;c__Actinomycetia;o__Nanopelagicales;f__Nanopelagicaceae;g__PALSA-747	95.0	N/A	N/A	N/A	N/A	1	-
--------------------------------------------------------------------------------
[2023-06-30 20:55:53,152] [INFO] GTDB search result was written to GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/result_gtdb.tsv
[2023-06-30 20:55:53,155] [INFO] ===== GTDB Search completed =====
[2023-06-30 20:55:53,159] [INFO] DFAST_QC result json was written to GCA_903845795.1_freshwater_MAG_---_Umea2p2_bin-0836_genomic.fna/dqc_result.json
[2023-06-30 20:55:53,159] [INFO] DFAST_QC completed!
[2023-06-30 20:55:53,160] [INFO] Total running time: 0h0m31s